check df for tipdated models

check add_edge_length for tipdated data

rate model:
 * fix df
 * fix print method, guess model

test plotBS speziel bei rooted trees

read.phyDat type="USER" , levels=...   DONE

rell bootstrap (Ultrafast Bootstrap) testing  TODO


summary_edges

vignettes discrete


ancestral
as.phyDat für non-DNA mit [] und contrast für parsimony, export als nexus file
"array" output
add nodelabels an results


test1 <- ancestral.pars(tree, Laurasiatherian, "ACCTRAN", return = "phyDat")
test3 <- ancestral.pars(tree, Laurasiatherian, "POSTORDER", return = "phyDat")

# fixed
test2 <- ancestral.pars(tree, Laurasiatherian, "MPR", return = "phyDat")



unique.multiPhylo, ratchet + stochastic adding
mit hash.phylo


fix optRooted towards the root!!!
phylo.R#1547


createLabels
addConfidencesMultiPhylo
addConfidences.networx
addConfidences.multiPhylo
presenceAbsence
coords


matchEdges raus?? in bootstrap.R


checks:
  parsimony: RI, CI document
             old2new raus???

  phylo:     optimF3x4
             init_rell, rell

  networx:   addConfidencesMultiPhylo, createLabel, addConfidences.multiPhylo,
             presenceAbsence
             coords
             closest.edge, closest.node

  phyDat:    removeUndeterminedSites

  ancestral_pml: ancestral.pars mit allen Varianten

  splitsNetwork

  treeManipulation: midpoint.multiPhylo, pruneTree

  read.phyDat mit nexus format

  bug fixes:

  fitch.spr both sides und openMP

  pmlMix



optim.pml mit empirical statt estimated als default.
check my gamma distributions


